If excessive manure adds cations like potassium, calcium, and sodium to the soil, then the pH would naturally go up.  Lime would not be needed if that's the case.  Is lime being applied to highly manured fields in your area?

Is the concern that because of higher manure applications (that contain organic matter) the rich dark soils are getting lighter?

Or that the rich dark soils are becoming like the lighter, CaCO3-high soils due to manure application?

Sorry, a lot to question on this one...